What signs are you seeing in the sick birds? If there is a chronic respiratory disease in your flock, it will remain there for the life of your flock. Any chickens exposed will be carriers for life, and MG affects other species such as ducks, quail, turkeys, etc. Once these chickens are all gone from your environment, the disease will die out after several days, since it lasts only 3 days outside the chicken or other host. That said, if wild birds are feeding out of your feeders and waterers, they can keep spreading it. If you have a very sick chicken, you may want to put it down, and get a necropsy done by the state poultry lab to find out what disease they are getting.
Gapeworm is fairly rare. A fecal test done by your local vet on some fresh droppings, can help identify any worms or larvae. It can be treated with fendbendazole (Safeguard Liquid Goat wormer) given for 3-5 days to each chicken, at a dose of 1/4 ml per pound.
Other good wormers are Valbazen 1/2 ml once to each chicken, and then repeat in 10 days. Wormout Gel can be used in the water for 2 whole days to treat the flock, as the only water source.